Nicotinic acid hydroxylase (NAH) from Clostridium barkeri and formate dehydrogenase H (FDH) from Escherichia coli are selenium and molybdenum containing enzymes. NAH contains Se in a non-identified cofactor form, whereas FDH contains Se as selenocysteine (SeCys-140) residue. Previously, we have shown that Se of NAH is coordinated with Mo and is essential for hydroxylation of nicotinate. We show now that the Se atom of SeCys is coordinated with Mo in FDH and that this coordination is important for formate oxidation. From the sequence homology we conclude that other molybdopterin-containing procaryotic enzymes also have amino acids ligated to Mo and the identities of these amino acids are predicted. A Se-containing and two Se-deficient NAH isozymes were characterized in detail. These data suggest novel metabolic pathways for Se in Clostridia and certain other bacteria. Mechanistic and structural information obtained from EPR and ENDOR studies reveal some aspects of the mechanisms for substrate oxidation in NAH and FDH and the structures of SeMo active centers of these enzymes.